Pipe joint addon: changing individual cylinder's geometry (radius, length)
The geometry of the objects added from the pipe joint addon is the same as any of the other items, whether from the primitives menus, or added by a user, and can be manipulated the same way. Portions of meshes which align neatly with one of the primary axes, in the case of the pipe joint "y", the base which aligns with the z axis are fairly easy. Make a couple of loop cuts, slide them up the cylinder to where you want them, scale them to zero in the appropriate direction (in the case of the base cylinder, this would be "z"), then lock the z axis and scale them to size on the x and y axes. 

When the case of the arms of the y-joint, it is a bit more difficult for me, as I've not figured out a good way to move items along an axis which was not parallel to one of the principal axes. With to my current skillset, my procedure is illustrated by this image:



where I use "helper geometry" to get the alignment correct. Sharp eyes may note that in the illustration in step 10 I've not yet removed the helper geometry, but it's trivial to do, selecting the helper geometry edge in edge select mode, and removing the edge only. 

Another option, is, of course, to rotate the whole mesh at the beginning so that the axis you want to change is aligned with the x, y, or z axis, and use the simpler procedure outlined above. 

Finally a workflow comment: if you are using a lot of modified pipe joints, I'd keep the modifications in a separate blend file, as separate objects, and import them to your working file by appending them. Once you've got one modified y joint with an enlarged arm on one side, it's trivial to create a new instance of that joint, and change the size of the arm for a different location in your mesh.